If you go to the package listing page, on the left hand side are a set of 'biocViews', one of which is StatisticalMethod. Machine learning is a broad category that encompasses several of the methods there, but you should be able to look through the choices and see which package(s) are applicable.
perhaps you are referring to characteristics of RNA-Seq data that make it necessary to "preprocess" the data before applying regular ML methods: normalisation for library size and transformation to make the data less skewed and less heteroskedastic. Have a look at the variance stabilizing transformation in DESeq2. It's also described in the vignette.
Hope this helps